rs2385686

Positions:

• chr8-126647291-A-G
• chr8-126647291-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000645463.1(PCAT1):​n.283+54873A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,676 control chromosomes in the GnomAD database, including 17,105 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (17105 hom., cov: 30)
• Consequence: PCAT1 ENST00000645463.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

Genes affected

PCAT1 (HGNC:43022): (prostate cancer associated transcript 1) This gene produces a long non-coding RNA that promotes cell proliferation and is upregulated in prostate, colorectal, and other cancers. This RNA negatively regulates the BRCA2 tumor suppressor protein and positively regulates Myc oncoprotein. It contains binding sites for microRNAs, and may act as a sponge for microRNAs that regulate cell growth pathways. [provided by RefSeq, Dec 2017]

LOC105375751 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375751	XR_007061097.1	n.1389-65995A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCAT1	ENST00000645463.1	n.283+54873A>G		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000519880.5	n.156+58001A>G		intron_variant, non_coding_transcript_variant		4
PCAT1	ENST00000520512.1	n.137-19254A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71046 AN: 151556 Hom.: 17102 Cov.: 30

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.440

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.468 AC: 71056 AN: 151676 Hom.: 17105 Cov.: 30 AF XY: 0.479 AC XY: 35484 AN XY: 74096

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.443

Alfa AF: 0.467 Hom.: 24145

Bravo AF: 0.451

Asia WGS AF: 0.570 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2385686; hg19: chr8-127659536;